Re: problems installing openmpi_ext

[Alexander Hansen]

On 8/12/13 5:26 AM, Francis Poulin wrote:
> Hello,
>
> Sorry for the quick send before.  I have looked into the problem and see all 
> the dependencies are installed and even loaded (probably not necessary).
>
> octave:20> pkg list
> Package Name  | Version | Installation directory
> --------------+---------+-----------------------
>           bim *|   1.1.2 | /Users/fpoulin/octave/bim-1.1.2
>           fpl *|   1.3.4 | /Users/fpoulin/octave/fpl-1.3.4
>           msh *|   1.0.8 | /Users/fpoulin/octave/msh-1.0.8
>      parallel *|   2.0.5 | /Users/fpoulin/octave/parallel-2.0.5
>       splines *|   1.2.2 | /Users/fpoulin/octave/splines-1.2.2
>
> Now that I try and install openmpi_ext I get the following error
>
> octave:22> pkg install openmpi_ext-1.1.0.tar.gz
> MPI_Iprobe.cc: In function 'Octave_map put_MPI_Stat(const MPI_Status&)':
> MPI_Iprobe.cc:38:14: error: 'const struct MPI_Status' has no member named 
> '_count'
> make: *** [MPI_Iprobe.oct] Error 1
> 'make' returned the following error: /opt/local/bin/mkoctfile-3.6.4 
> -I/sw/include/openmpi/opal/mca/hwloc/hwloc132/hwloc/include -I/sw/include 
> -I/sw/include/openmpi -L/sw/lib/openmpi -lmpi_cxx -lmpi -lm MPI_Init.cc
> /opt/local/bin/mkoctfile-3.6.4 
> -I/sw/include/openmpi/opal/mca/hwloc/hwloc132/hwloc/include -I/sw/include 
> -I/sw/include/openmpi -L/sw/lib/openmpi -lmpi_cxx -lmpi -lm MPI_Initialized.cc
> /opt/local/bin/mkoctfile-3.6.4 
> -I/sw/include/openmpi/opal/mca/hwloc/hwloc132/hwloc/include -I/sw/include 
> -I/sw/include/openmpi -L/sw/lib/openmpi -lmpi_cxx -lmpi -lm MPI_Comm_rank.cc
> /opt/local/bin/mkoctfile-3.6.4 
> -I/sw/include/openmpi/opal/mca/hwloc/hwloc132/hwloc/include -I/sw/include 
> -I/sw/include/openmpi -L/sw/lib/openmpi -lmpi_cxx -lmpi -lm MPI_Comm_size.cc
> /opt/local/bin/mkoctfile-3.6.4 
> -I/sw/include/openmpi/opal/mca/hwloc/hwloc132/hwloc/include -I/sw/include 
> -I/sw/include/openmpi -L/sw/lib/openmpi -lmpi_cxx -lmpi -lm MPI_Finalize.cc
> /opt/local/bin/mkoctfile-3.6.4 
> -I/sw/include/openmpi/opal/mca/hwloc/hwloc132/hwloc/include -I/sw/include 
> -I/sw/include/openmpi -L/sw/lib/openmpi -lmpi_cxx -lmpi -lm MPI_Finalized.cc
> /opt/local/bin/mkoctfile-3.6.4 
> -I/sw/include/openmpi/opal/mca/hwloc/hwloc132/hwloc/include -I/sw/include 
> -I/sw/include/openmpi -L/sw/lib/openmpi -lmpi_cxx -lmpi -lm MPI_Send.cc
> /opt/local/bin/mkoctfile-3.6.4 
> -I/sw/include/openmpi/opal/mca/hwloc/hwloc132/hwloc/include -I/sw/include 
> -I/sw/include/openmpi -L/sw/lib/openmpi -lmpi_cxx -lmpi -lm MPI_Recv.cc
> /opt/local/bin/mkoctfile-3.6.4 
> -I/sw/include/openmpi/opal/mca/hwloc/hwloc132/hwloc/include -I/sw/include 
> -I/sw/include/openmpi -L/sw/lib/openmpi -lmpi_cxx -lmpi -lm MPI_Iprobe.cc
> error: called from 'pkg>configure_make' in file 
> /opt/local/share/octave/3.6.4/m/pkg/pkg.m near line 1385, column 9
> error: called from:
> error:   /opt/local/share/octave/3.6.4/m/pkg/pkg.m at line 827, column 5
> error:   /opt/local/share/octave/3.6.4/m/pkg/pkg.m at line 383, column 9
>
> I have two versions of octave installed, one through macports and the other 
> through fink. Maybe there is a conflict somewhere?  If there is an easier way 
> to install it in my mac that would be great to know.
>
> Cheers, Francis
> _______________________________________________

For Fink, you can use "fink install openmpi-ext-oct364"  (assuming that 
your Fink Octave is 3.6.4).  I can't speak for what you'd do via Macports.

I recommend installing Octave Forge packages through a package manager 
if you don't need an SVN/hg version, in any case.  We handle 
dependencies from outside of Octave, which the "pkg" command by itself 
can't do (yet), and we can patch builds that don't work for whatever 
reason:  library API changes, constructions that don't exist on OS X, etc.

In the case of what you're seeing, it looks like you've got an OpenMPI 
installed which doesn't know about _count (>=1.5).  Fink's openmpi_ext 
packaging patches for this very issue.
--
Alexander Hansen, Ph.D.
Fink User Liaison
My package updates: http://finkakh.wordpress.com/